gromacs

About

GROMACS is a versatile
package to perform molecular dynamics, i.e. simulate the Newtonian
equations of motion for systems with hundreds to millions of
particles. It is primarily designed for biochemical molecules like
proteins and lipids that have a lot of complicated bonded
interactions, but since GROMACS is extremely fast at calculating
the nonbonded interactions (that usually dominate simulations)
many groups are also using it for research on non-biological
systems, e.g. polymers.

Versions and Availability

Softenv Keys for gromacs on tezpur

▶ Softenv FAQ?

Shells

A user may choose between using /bin/bash
and /bin/tcsh. Details about each shell follows.

/bin/bash

System resource file: /etc/profile

When one access the shell, the following user files are read in if
they exist (in order):

~/.bash_profile (anything sent to STDOUT or STDERR
will cause things like rsync to break)

~/.bashrc (interactive login only)

~/.profile

When a user logs out of an interactive session, the
file ~/.bash_logout is executed if it exists.

The default value of the environmental variable, PATH, is
set automatically using SoftEnv. See below for more
information.

/bin/tcsh

The file ~/.cshrc is used to customize the user's
environment if his login shell is /bin/tcsh.

Softenv

SoftEnv is a utility that is supposed to help users manage complex
user environments with potentially conflicting application versions
and libraries.

System Default Path

When a user logs in, the system /etc/profile
or /etc/csh.cshrc (depending on login shell, and mirrored
from csm:/cfmroot/etc/profile)
calls /usr/local/packages/softenv-1.6.2/bin/use.softenv.sh to
set up the default path via the SoftEnv database.

SoftEnv looks for a user's ~/.soft file and updates the
variables and paths accordingly.

Viewing Available Packages

The command softenv will provide a list of
available packages. The listing will look something like:

Managing SoftEnv

The file ~/.soft in the user's home directory is where
the different packages are managed. Add the +keyword into your .soft
file. For instance, ff one wants to add the Amber Molecular Dynamics
package into their environment, the end of the .soft file should look
like this:

+amber-8

@default

To update the environment after modifying this file, one simply
uses the resoft command:

% resoft

The command soft can be used to manipulate the environment
from the command line. It takes the form:

$ soft add/delete +keyword

Using this method of adding or removing keywords requires the user
to pay attention to possible order dependencies. That is, best results
require the user to remove keywords in the reverse order in which they
were added. It is handy to test out individual keys, but can lead to
trouble if changing multiple keys. Changing the .soft file and
issuing the resoft is the recommended way of dealing with
multiple changes.

▶ QSub FAQ?

Portable Batch System: qsub

qsub

All HPC@LSU clusters use the Portable Batch System (PBS) for
production processing. Jobs are submitted to PBS using the qsub
command. A PBS job file is basically a shell script which also
contains directives for PBS.

Usage

$ qsub job_script

Where job_script is the name of the file containing the script.

PBS Directives

PBS directives take the form:

#PBS -X value

Where X is one of many single letter options, and value is the
desired setting. All PBS directives must appear before any active
shell statement.

Example Job Script

#!/bin/bash
#
# Use "workq" as the job queue, and specify the allocation code.
#
#PBS -q workq
#PBS -A your_allocation_code
#
# Assuming you want to run 16 processes, and each node supports 4 processes,
# you need to ask for a total of 4 nodes. The number of processes per node
# will vary from machine to machine, so double-check that your have the right
# values before submitting the job.
#
#PBS -l nodes=4:ppn=4
#
# Set the maximum wall-clock time. In this case, 10 minutes.
#
#PBS -l walltime=00:10:00
#
# Specify the name of a file which will receive all standard output,
# and merge standard error with standard output.
#
#PBS -o /scratch/myName/parallel/output
#PBS -j oe
#
# Give the job a name so it can be easily tracked with qstat.
#
#PBS -N MyParJob
#
# That is it for PBS instructions. The rest of the file is a shell script.
#
# PLEASE ADOPT THE EXECUTION SCHEME USED HERE IN YOUR OWN PBS SCRIPTS:
#
# 1. Copy the necessary files from your home directory to your scratch directory.
# 2. Execute in your scratch directory.
# 3. Copy any necessary files back to your home directory.
# Let's mark the time things get started.
date
# Set some handy environment variables.
export HOME_DIR=/home/$USER/parallel
export WORK_DIR=/scratch/myName/parallel
# Set a variable that will be used to tell MPI how many processes will be run.
# This makes sure MPI gets the same information provided to PBS above.
export NPROCS=`wc -l $PBS_NODEFILE |gawk '//{print $1}'`
# Copy the files, jump to WORK_DIR, and execute! The program is named "hydro".
cp $HOME_DIR/hydro $WORK_DIR
cd $WORK_DIR
mpirun -machinefile $PBS_NODEFILE -np $NPROCS $WORK_DIR/hydro
# Mark the time processing ends.
date
# And we're out'a here!
exit 0